Re: Enhance electrostatic interactions?

From: daniel aguayo (bioquimico_at_gmail.com)
Date: Fri Oct 22 2010 - 16:34:19 CDT

Wendy
Actualmente tienes el parametro fullelecfrq en 2 pues
debes multiplcarlo por el timestep.. luego si el archivo de conf
dice

timestep 0.5
rigidBonds all
nonbondedFreq 2
fullElectFrequency 4
stepspercycle 20

significa para uno
timestep 0.5
rigidBonds all
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 20

Saludos
DAV
HSP la elegiste por que? puede ser que la interaccion se de por otro estado
de protonacion
de la HIS, refiriendome a la ubicacion del proton a deprotonar/protonar?

2010/10/21 Wendy González <locuswendy_at_gmail.com>

> Dear all:
>
> I am studying a system where one GLU seem to have a electrostatic
> interaction with one HSP that is nearby. But, in my MD simulations this
> interaction (that should bring the HSP closed to the GLU) is not taking
> place. Can I enhance the electrostatic field of this GLU or can I make my MD
> with fullelectfreq = 2 to see this phenomena??? My Integrator Parameters
> are:
> timestep 0.5
> rigidBonds all
> nonbondedFreq 2
> fullElectFrequency 4
> stepspercycle 20
>
> Thanks for your answers,
> Wendy
>

-- 
saludos desde el fin del mundo

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